ChIP-seq accurately predicts tissue-specific activity of enhancers

A major yet unresolved quest in decoding the human genome is the identification of the regulatory sequences that control the spatial and temporal expression of genes. Distant-acting transcriptional enhancers are particularly challenging to uncover because they are scattered among the vast non-coding portion of the genome. Evolutionary sequence constraint can facilitate the discovery of enhancers, but fails to predict when and where they are active in vivo. Here we present the results of chromatin immunoprecipitation with the enhancer-associated protein p300 followed by massively parallel sequencing, and map several thousand in vivo binding sites of p300 in mouse embryonic forebrain, midbrain and limb tissue. We tested 86 of these sequences in a transgenic mouse assay, which in nearly all cases demonstrated reproducible enhancer activity in the tissues that were predicted by p300 binding. Our results indicate that in vivo mapping of p300 binding is a highly accurate means for identifying enhancers and their associated activities, and suggest that such data sets will be useful to study the role of tissue-specific enhancers in human biology and disease on a genome-wide scale.

[1]  D. Mccormick.  Sequence the Human Genome , 1986, Bio/Technology.

[2]  J. Rossant,et al.  A transgene containing lacZ inserted into the dystonia locus is expressed in neural tube , 1988, Nature.

[3]  Michael R. Green,et al.  Nuclear protein CBP is a coactivator for the transcription factor CREB , 1994, Nature.

[4]  J B Lawrence,et al.  Molecular cloning and functional analysis of the adenovirus E1A-associated 300-kD protein (p300) reveals a protein with properties of a transcriptional adaptor. , 1994, Genes & development.

[5]  S. Brenner,et al.  A conserved retinoic acid response element required for early expression of the homeobox gene Hoxb-1 , 1994, Nature.

[6]  B. Howard,et al.  The Transcriptional Coactivators p300 and CBP Are Histone Acetyltransferases , 1996, Cell.

[7]  D. Livingston,et al.  Interaction and functional collaboration of p300/CBP and bHLH proteins in muscle and B-cell differentiation. , 1996, Genes & development.

[8]  S. Karlin,et al.  Prediction of complete gene structures in human genomic DNA. , 1997, Journal of molecular biology.

[9]  David Newsome,et al.  Gene Dosage–Dependent Embryonic Development and Proliferation Defects in Mice Lacking the Transcriptional Integrator p300 , 1998, Cell.

[10]  M. Merika,et al.  Recruitment of CBP/p300 by the IFN beta enhanceosome is required for synergistic activation of transcription. , 1998, Molecular cell.

[11]  Dimitris Thanos,et al.  Ordered Recruitment of Chromatin Modifying and General Transcription Factors to the IFN-β Promoter , 2000, Cell.

[12]  International Human Genome Sequencing Consortium.  Initial sequencing and analysis of the human genome , 2001, Nature.

[13]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[14]  Mouse Genome Sequencing Consortium.  Initial sequencing and comparative analysis of the mouse genome , 2002, Nature.

[15]  B. Spiegelman,et al.  Transcription coactivator TRAP220 is required for PPARγ2-stimulated adipogenesis , 2002, Nature.

[16]  Colin N. Dewey,et al.  Initial sequencing and comparative analysis of the mouse genome. , 2002 .

[17]  B. Spiegelman,et al.  Transcription coactivator TRAP220 is required for PPAR gamma 2-stimulated adipogenesis. , 2002, Nature.

[18]  E. Birney,et al.  Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs , 2002, Nature.

[19]  M. Nóbrega,et al.  Scanning Human Gene Deserts for Long-Range Enhancers , 2003, Science.

[20]  Michael Q. Zhang,et al.  A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[21]  Leah Barrera,et al.  A high-resolution map of active promoters in the human genome , 2005, Nature.

[22]  Klaudia Walter,et al.  Open access, freely available online PLoS BIOLOGY Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development , 2022 .

[23]  J. Tena,et al.  A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts. , 2005, Genome research.

[24]  D. Haussler,et al.  Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. , 2005, Genome research.

[25]  Daniel J. Blankenberg,et al.  Galaxy: a platform for interactive large-scale genome analysis. , 2005, Genome research.

[26]  Michael R. Green,et al.  Transcriptional regulatory elements in the human genome. , 2006, Annual review of genomics and human genetics.

[27]  T. Tatusova,et al.  NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2006, Nucleic Acids Research.

[28]  Shyam Prabhakar,et al.  Close sequence comparisons are sufficient to identify human cis-regulatory elements. , 2005, Genome research.

[29]  E. Ukkonen,et al.  Genome-wide Prediction of Mammalian Enhancers Based on Analysis of Transcription-Factor Binding Affinity , 2006, Cell.

[30]  Alan M. Moses,et al.  In vivo enhancer analysis of human conserved non-coding sequences , 2006, Nature.

[31]  Ivan Ovcharenko,et al.  Predicting tissue-specific enhancers in the human genome. , 2006, Genome research.

[32]  Jane M J Lin,et al.  Identification and Characterization of Cell Type–Specific and Ubiquitous Chromatin Regulatory Structures in the Human Genome , 2007, PLoS genetics.

[33]  T. Mikkelsen,et al.  Genome-wide maps of chromatin state in pluripotent and lineage-committed cells , 2007, Nature.

[34]  Inna Dubchak,et al.  VISTA Enhancer Browser—a database of tissue-specific human enhancers , 2006, Nucleic Acids Res..

[35]  Colin N. Dewey,et al.  Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. , 2007, Genome research.

[36]  William Stafford Noble,et al.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project , 2007, Nature.

[37]  Allen D. Delaney,et al.  Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing , 2007, Nature Methods.

[38]  Bronwen L. Aken,et al.  Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences , 2007, Nature.

[39]  Tatiana Tatusova,et al.  NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2004, Nucleic Acids Res..

[40]  Nathaniel D. Heintzman,et al.  Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome , 2007, Nature Genetics.

[41]  N. D. Clarke,et al.  Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells , 2008, Cell.

[42]  Anthony P. Fejes,et al.  Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding. , 2008, Genome research.

[43]  Nicholas H. Putnam,et al.  The amphioxus genome illuminates vertebrate origins and cephalochordate biology. , 2008, Genome research.

[44]  Michael Q. Zhang,et al.  Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs. , 2007, Genome research.

[45]  Christopher D. Brown,et al.  Qualifying the relationship between sequence conservation and molecular function. , 2008, Genome research.

[46]  A. Kania,et al.  Identification of genes controlled by LMX1B in the developing mouse limb bud , 2008, Developmental dynamics : an official publication of the American Association of Anatomists.

[47]  Michael A. Beer,et al.  Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b. , 2008, Genome research.

[48]  Thomas Zeng,et al.  Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing , 2008, Nucleic acids research.

[49]  S. Batzoglou,et al.  Genome-Wide Analysis of Transcription Factor Binding Sites Based on ChIP-Seq Data , 2008, Nature Methods.

[50]  Tao Zhang,et al.  Identification of ancient remains through genomic sequencing. , 2008, Genome research.

[51]  Z. Weng,et al.  High-Resolution Mapping and Characterization of Open Chromatin across the Genome , 2008, Cell.

[52]  Francesca Chiaromonte,et al.  Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif. , 2008, Genome research.

[53]  Dustin E. Schones,et al.  Genome-wide approaches to studying chromatin modifications , 2008, Nature Reviews Genetics.

[54]  A. Visel,et al.  Ultraconservation identifies a small subset of extremely constrained developmental enhancers , 2008, Nature Genetics.

[55]  Dustin E. Schones,et al.  Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. , 2008, Genome research.